4.0.0-7

Probably the biggest new feature, this lets you organise your Home Menu with folders. Here's how they work.
Select an unoccupied tile and select "Create Folder".
Tap "Edit Settings" if you want to name your folder, but remember: only the first letter shows up on its Home Menu icon. The full name appears on the top screen when you tap the folder.
Press your stylus onto an icon for a second and you'll 'pick it up'.
Drag it over to the folder and take your stylus off the screen to 'drop' the icon into the folder.
That's pretty much all there is to it. You can't put folders inside other folders, so don't try to nest them.

The other most noticeable improvement is to the eShop. Here's what's new:

New layout — now split into two rows, the bottom is for easy access to 3DS Download Software, 3DS Virtual Console, DSiWare and 3DS Demos, while the top row is for the usual curated list and 'themes'. The search bar is now at the top, too.

QR Code option — the 3DS has been able to scan QR codes for ever, but now the eShop gives you a bespoke option. Tap this in the Settings/Other menu, scan a QR code and it'll open the relevant page in the eShop.

Download Later - You can now choose to download later when downloading. Meaning you can decide to download later after you chose to download it (kind of a cancel button for downloading).

Ability to patch games

This is a big one. Nintendo has added the ability for games — both retail and download — to receive updates in the form of patches or free add-on content. Here's what will be available in future.
Mario Kart 7 will get an update to address glitches. This update will be released in May, so don't go looking for it now.
Mighty Switch Force! will get five extra levels and a quick-retry button, all for free.

ErrDisp updated

ErrDisp was updated however it's unknown what changed. When the ARM11 kernel terminates an application process including when it crashed, the system now returns to Home Menu. Prior to this update, the system hanged when application processes terminated.

TWL_FIRM updated

TWL_FIRM and the whitelist was updated, blocking the savegame exploits for Cooking Coach and Classic Word Games, and blocked flash cards.